Eric, Just adding to Murat's excellent advice here: the quadratic edge collapse function in Meshlab is very useful for reducing file size of 3D objects. For my work, I specify a target of 500,000 faces and that gives me a good balance between not losing too much information in the object, but reducing the object to a manageable file size for downstream analysis (e.g., reading into R via geomorph, or the IDAV landmark editor program).
Some colleagues and I put together a workflow for processing and analyzing CT data using the programs Fiji and 3D Slicer, both of which are open-source and cross platform. The workflow is built around working with CT data, but includes step-by-step instruction for cleaning up and exporting 3D models in 3D Slicer (Steps 7b, 7c, and 7d), as well as video tutorials in the supplemental materials that demonstrate 3D model simplification and file conversion using Meshlab (Supplementary Video S3), which may be useful in your work. The workflow is available for free from the open access journal, Integrative Organismal Biology here <https://academic.oup.com/iob/article/2/1/obaa009/5818881> (https://doi.org/10.1093/iob/obaa009). I hope that helps and best of luck, Thaddaeus Buser On Friday, August 28, 2020 at 8:42:29 PM UTC-7 [email protected] wrote: > Eric, > > These are all excellent questions to ponder about, particularly when you > are starting with 3D digitization and morphometrics. Questions you ask > require validation. The first one, stitching of individual mesh elements to > form a 3D object, is the hardest one to quantify, because it requires an > independently acquired image of the same object at a high-resolution > (preferably with a modality like tomography) so that you can treat that as > a gold reference. Or you might consider scanning an object of known > dimensions (e.g., sphere, cube), and then you can compare your results from > geometric estimates (of volume, area) to the digitized one. From there it > is somewhat easy to generate heatmaps that will let you visualize the > difference between your gold-reference and your digitization. Once you > establish this flow, you can then experiment with your different algorithms > of stitching and/or data acquisition. > > The approach in the second part of the question is the same, but it is > easier because that point your original mesh would be the reference. Then > you can experiment with de-noising, smoothing, and remeshing steps and keep > comparing those to your original mesh to understand the effects of it. I am > not entirely sure if there is strict order applying the filters, it is more > about the end result really. I think for stereophotogrammetry steps more > like fuse, repair, clean. Whether you need remeshing or smoothing (or both) > will be dependent on your downstream pipeline (e.g., if the tool you are > using expecting fairly uniformly distributed polygons to create semi > landmark, you will probably need to remesh). > > Again these are all empirical test, and you shouldn't take anybody > (including mine) as gospel to follow strictly, the idea is to experiment > and see the results for your particular data. Meshlab is very powerful for > this, but some of these (particularly some of the clean up tasks) can be > accomplished fairly easily in 3D Slicer using as well. For a conceptually > similar exercise on the effect of decimation to mesh geometry you can take > a look at this tutorial from our recent workshop. > > https://github.com/SlicerMorph/S_2020/blob/master/Day_4/Surface_Toolbox/Mesh_edits.md > > HTH, > M > > On Friday, August 28, 2020 at 5:27:25 PM UTC-7 [email protected] wrote: > >> Hello everyone, >> >> I'm just starting out in 3D GM and I'm really stuck when it comes to >> figuring out a workflow for producing 3D surface meshes that are de-noised >> without losing topological integrity, making them suitable for analysis. >> >> I've been using a NextEngine Ultra HD laser scanner for producing scans. >> I've then been moving the scans into Meshlab to to do everything else, from >> aligning and fusing to repairing and smoothing. I've come to view the >> number of filters in Meshlab to be both a blessing and a curse. I've also >> looked into MeshMixer, but everything seems to be black-boxed, and that >> make me a little uneasy. >> >> I'm also confused as to the order of steps. Should I fuse my scans and >> then clean and repair, or vice versa? What is the best way to de-noise? >> Should I smooth or remesh? In what order should I be applying filters? >> >> I'm hoping that someone here might be able to suggest a workflow to guide >> me through the process or direct me to some publications that can answer >> all of my questions. Also feel free to suggest some other 3D mesh >> applications that I'm likely not aware of. >> >> Any advice would be greatly appreciated. Thanks everyone! >> >> Best, >> Eric >> > -- You received this message because you are subscribed to the Google Groups "Morphmet" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/morphmet2/d9f447bc-2555-424d-8cd6-d9738787c496n%40googlegroups.com.
